Java ResolvedConceptReferenceList.getResolvedConceptReference方法代码示例

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public void dumpResolvedValueSetCodingSchemes() {
	int sample_size = 5;
	Vector v = getResolvedValueSetCodingSchemes();
	System.out.println("\nNumber of Resolved Value Set coding schemes: " + v.size());
       for (int i=0; i<5; i++) {
		String t = (String) v.elementAt(i);
		int j = i+1;
		System.out.println("\n" + " (" + j + ") " + t);

		String cs_name = getValueSetCodingSchemeName(t);
		String cs_version = getValueSetCodingSchemeVersion(t);
		System.out.println("\t" + cs_name + " (" + cs_version + ")");

		ResolvedConceptReferenceList samples = generateTestCases(cs_name, cs_version, sample_size, TestCaseGenerator.TYPE_VALUE_SET);
		for (int k=0; k<samples.getResolvedConceptReferenceCount(); k++) {
			ResolvedConceptReference rcr = (ResolvedConceptReference) samples.getResolvedConceptReference(k);
			System.out.println("\t" + rcr.getEntityDescription().getContent() + " (" + rcr.getCode() + ")");
		}
	}
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
private ResolvedConceptReferenceList addEntities(
        ResolvedConceptReferenceList unresolvedList,
        List<CodeToReturn> codesToReturn,
        LocalNameList restrictToProperties, PropertyType[] restrictToPropertyTypes) throws LBInvocationException {
    Map<String,Entity> entityMap = this.buildCodedEntry(
            codesToReturn,
            restrictToProperties,
            restrictToPropertyTypes);
    
    for(ResolvedConceptReference ref : unresolvedList.getResolvedConceptReference()) {
        if(ref == null) {continue;}
        
        String refKey = this.getKey(ref);
        ref.setEntity(entityMap.get(refKey));
    }
    
    return unresolvedList;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
/**
 * Prints the.
 *
 * @param cng the cng
 */
public static void print(CodedNodeGraph cng) {

	ResolvedConceptReferenceList rcrl;
	try {
		rcrl = cng.resolveAsList(null, false, true, 0, 0, null, null, null,
				-1);
		ResolvedConceptReference[] rcrArray = rcrl
				.getResolvedConceptReference();
		for (ResolvedConceptReference rcr : rcrArray) {
			print(rcr);
		}
	} catch (Exception e) {
		throw new RuntimeException(e);
	}
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public static void main(String[] args) throws Exception {
    args = parse(args);
    LexBIGService lbs = RemoteServerUtil.createLexBIGService();
    
    CodedNodeSet cns =
        lbs.getCodingSchemeConcepts("NCI MetaThesaurus", null);
    cns =
        cns.restrictToMatchingDesignations("single dose",
            SearchDesignationOption.ALL, "LuceneQuery", null);

    CodedNodeGraph cng = lbs.getNodeGraph("NCI MetaThesaurus", null, null);
    cng = cng.restrictToTargetCodes(cns);
    ResolvedConceptReferenceList list =
        cng.resolveAsList(null, true, false, 0, 0, null, null, null, null,
            500);

    for (ResolvedConceptReference ref : list.getResolvedConceptReference()) {
        System.out.println("Code: " + ref.getCode());
        System.out.println(" Entity Description"
            + ref.getEntityDescription().getContent());
    }
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
/**
 * Display name and description information for the given cui.
 * @param code
 * @param lbSvc
 * @param scheme
 * @param csvt
 * @return A fully resolved concept reference for the code.
 * @throws LBException
 */
protected ResolvedConceptReference printCode(String cui, EVSApplicationService lbSvc, String scheme, CodingSchemeVersionOrTag csvt)
		throws LBException
{
	// Locate the matching concept ...
	CodedNodeSet cns = lbSvc.getCodingSchemeConcepts(scheme, csvt);
	cns.restrictToMatchingProperties(
			ConvenienceMethods.createLocalNameList("UMLS_CUI"),
			new PropertyType[] {PropertyType.GENERIC},
			cui,
			"exactMatch",
			null);
	ResolvedConceptReferenceList cnsList = cns.resolveToList(
			null, // sort options
			null, // property names
			new PropertyType[] {PropertyType.PRESENTATION}, // property types
			1);
	if (cnsList.getResolvedConceptReferenceCount() == 0) {
		Util.displayMessage("Unable to find code for CUI = '" + cui + "'");
		return null;
	}
	ResolvedConceptReference rcr = cnsList.getResolvedConceptReference(0);
	Util.displayMessage("Concept code: " + rcr.getConceptCode());
	Util.displayMessage("Description : " + rcr.getEntityDescription().getContent());

	return rcr;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public ResolvedConceptReference buildResolvedConceptReference(CodeToReturn codeToReturn,
        LocalNameList restrictToProperties, PropertyType[] restrictToPropertyTypes, Filter[] filters,
        boolean resolve) throws LBInvocationException {
    ResolvedConceptReferenceList returnList = this.buildResolvedConceptReference(
            DaoUtility.createNonTypedList(codeToReturn), restrictToProperties, restrictToPropertyTypes, filters, resolve);
   
    Assert.state(returnList.getResolvedConceptReferenceCount() <= 1);
    
    if(returnList.getResolvedConceptReferenceCount() == 1) {
        return returnList.getResolvedConceptReference(0);
    } else {
        return null;
    }
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
/**
 * Resolve the Iterator
 *
 * @param iterator
 * @param maxToReturn
 * @param code
 * @return
 */
public Vector<Entity> resolveIterator(
        ResolvedConceptReferencesIterator iterator, int maxToReturn,
        String code) {

    Vector<Entity> v = new Vector<Entity>();

    if (iterator == null) {
        _logger.warn("No match.");
        return v;
    }
    try {
        int iteration = 0;
        while (iterator.hasNext()) {
            iteration++;
            iterator = iterator.scroll(maxToReturn);
            ResolvedConceptReferenceList rcrl = iterator.getNext();
            ResolvedConceptReference[] rcra = rcrl
                    .getResolvedConceptReference();
            for (int i = 0; i < rcra.length; i++) {
                ResolvedConceptReference rcr = rcra[i];
                Entity ce = rcr.getReferencedEntry();
                if (code == null) {
                    v.add(ce);
                } else {
                    if (ce.getEntityCode().compareTo(code) != 0)
                        v.add(ce);
                }
            }
        }
    } catch (Exception e) {
        _logger.warn(e.getMessage());
    }
    return v;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public void generateViewInHierarchyTests() {
  String target = null;
  TestCase testCase = null;
  for (int i=0; i<browserHomeDisplayLabels.size(); i++) {
   String label = (String) browserHomeDisplayLabels.elementAt(i);
   String scheme = testUtils.getCodingSchemeName(label);
   String version = testUtils.getCodingSchemeVersion(label);
   boolean skip = true;
         if (scheme != null && scheme.compareTo(gov.nih.nci.evs.browser.common.Constants.NCI_METATHESAURUS) != 0 &&
             !Arrays.asList(gov.nih.nci.evs.browser.common.Constants.TERMINOLOGY_VALUE_SET_NAMES).contains(scheme)) {
	if (metadataUtils.tree_access_allowed(scheme, version)) {
	   ResolvedConceptReferenceList rcrl = testUtils.generateTestCases(scheme, version, ServiceTestCase.SAMPLE_SIZE, TestCaseGenerator.TYPE_TERMINOLOGY);
	   int n = rvGenerator.uniform(0, rcrl.getResolvedConceptReferenceCount()-1);
	   ResolvedConceptReference rcr = (ResolvedConceptReference) rcrl.getResolvedConceptReference(n);
	   String code = rcr.getConceptCode();
	   String name = rcr.getEntityDescription().getContent();

	   // code search
	   test_counter++;
	   int testNumber = test_counter;
	   String browserLink = label;
	   String algorithm = "exactMatch";
	   String matchText = code;
	   target = "codes";

	   testCase = testCaseWriter.createTestCase(testNumber, TestCase.VIEW_IN_HIERARCHY,
	   	                                      browserLink,
	   	                                      scheme, version, algorithm, target, matchText);
	   testCaseWriter.writeTestCase(testCase);
	   skip = false;
    }
      }
      if (skip) {
       System.out.println("\tView In Hierarchy -- " + scheme + " " + version + " skipped.");
}
 }
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public void printTestTermTypeDefinitionsHelp(PrintWriter out) {
 String method_name = "testTermTypeDefinitionsHelp";
 out.println("    @Test // (" + method_name + ")");
 out.println("    public void testTermTypeDefinitionsHelp() throws Exception {");
 out.println("		driver.get(baseUrl + \"/ncimbrowser/\");");
 String scheme = gov.nih.nci.evs.browser.common.Constants.NCI_METATHESAURUS;
 String version = NCIm_PROD_Version;

 //ResolvedConceptReferenceList testCases = testUtils.generateTestCases(scheme, version, 10, TestCaseGenerator.TYPE_TERMINOLOGY);
 ResolvedConceptReferenceList testCases = ncimTestCases;
 int n = rvGenerator.uniform(0, testCases.getResolvedConceptReferenceCount()-1);
 ResolvedConceptReference rcr = (ResolvedConceptReference) testCases.getResolvedConceptReference(n);

 if (rcr == null) {
  	System.out.println("ResolvedConceptReference is NULL -- return ");
 }
 String code = rcr.getConceptCode();
    out.println("        driver.findElement(By.xpath(\"//input[@name='algorithm'][@value='exactMatch']\")).click();");
 out.println("		driver.findElement(By.name(\"matchText\")).clear();");
 out.println("		driver.findElement(By.id(\"searchTarget1\")).click();");
 out.println("		driver.findElement(By.name(\"matchText\")).sendKeys(\"" + code + "\");");

    out.println("		driver.findElement(By.id(\"searchTerm:search\")).click();");
    out.println("		Thread.sleep(1000);");
    out.println("		driver.findElement(By.name(\"sdTab\")).click();");
    out.println("		Thread.sleep(1000);");
    out.println("		driver.findElement(By.cssSelector(\"img[alt=\\\"Term Type Definitions\\\"]\")).click();");

    out.println("		String bodyText = null;");
    out.println("		String matchedString = \"Abbreviation in any source vocabulary\";");
    out.println("		Thread.sleep(4000);");
    out.println("		bodyText = getPopupWindowBodyText(driver);");
    out.println("		assertTrue(bodyText.contains(matchedString));");
    out.println("		Thread.sleep(1000);    ");
 out.println("    }");
 out.println("");
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public void printTestSourceHelp(PrintWriter out) {
 String method_name = "testSourceHelp";
 out.println("    @Test // (" + method_name + ")");
 out.println("    public void testSourceHelp() throws Exception {");
 out.println("		driver.get(baseUrl + \"/ncimbrowser/\");");
 String scheme = gov.nih.nci.evs.browser.common.Constants.NCI_METATHESAURUS;
 String version = NCIm_PROD_Version;
 //ResolvedConceptReferenceList testCases = testUtils.generateTestCases(scheme, version, 10, TestCaseGenerator.TYPE_TERMINOLOGY);
 ResolvedConceptReferenceList testCases = ncimTestCases;//testUtils.generateTestCases(scheme, version, 10, TestCaseGenerator.TYPE_TERMINOLOGY);
 int n = rvGenerator.uniform(0, testCases.getResolvedConceptReferenceCount()-1);
 ResolvedConceptReference rcr = (ResolvedConceptReference) testCases.getResolvedConceptReference(n);
 if (rcr == null) {
  	System.out.println("ResolvedConceptReference is NULL -- return ");
 }
 String code = rcr.getConceptCode();
    out.println("        driver.findElement(By.xpath(\"//input[@name='algorithm'][@value='exactMatch']\")).click();");
 out.println("		driver.findElement(By.name(\"matchText\")).clear();");
 out.println("		driver.findElement(By.id(\"searchTarget1\")).click();");
 out.println("		driver.findElement(By.name(\"matchText\")).sendKeys(\"" + code + "\");");

    out.println("		driver.findElement(By.id(\"searchTerm:search\")).click();");
    out.println("		Thread.sleep(1000);");
    out.println("		driver.findElement(By.name(\"sdTab\")).click();");
    out.println("		Thread.sleep(1000);");
    out.println("		driver.findElement(By.cssSelector(\"img[alt=\\\"Source List\\\"]\")).click();");

    out.println("		String bodyText = null;");
    out.println("		String matchedString = \"National Cancer Institute Thesaurus\";");
    out.println("		Thread.sleep(4000);");
    out.println("		bodyText = getPopupWindowBodyText(driver);");
    out.println("		assertTrue(bodyText.contains(matchedString));");
    out.println("		Thread.sleep(1000);    ");
 out.println("    }");
 out.println("");
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public ResolvedConceptReferenceList generateResolvedConceptReferences(String codingScheme, String version, int number) {
	if (version == null) {
		version = codingSchemeDataUtils.getVocabularyVersionByTag(codingScheme, gov.nih.nci.evs.browser.common.Constants.PRODUCTION);
	}

       CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
       if (version != null) {
           csvt.setVersion(version);
	}

	ResolvedConceptReferenceList rcrl = new ResolvedConceptReferenceList();
	try {
		LocalNameList entityTypes = new LocalNameList();
		entityTypes.addEntry("concept");
		CodedNodeSet cns = lbSvc.getNodeSet(codingScheme, csvt, entityTypes);

		SortOptionList sortOptions = null;
		LocalNameList filterOptions = null;
		LocalNameList propertyNames = null;
		CodedNodeSet.PropertyType[] propertyTypes = null;
		boolean resolveObjects = false;
		int maxToReturn = number;
           ResolvedConceptReferenceList rvrlist = cns.resolveToList(sortOptions, filterOptions, propertyNames, propertyTypes, resolveObjects, maxToReturn);

           for (int i=0; i<rvrlist.getResolvedConceptReferenceCount(); i++) {
			ResolvedConceptReference rcr = rvrlist.getResolvedConceptReference(i);
			rcrl.addResolvedConceptReference(rcr);
		}
	} catch (Exception ex) {
		ex.printStackTrace();
	}
	return rcrl;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
protected List<? extends ResolvedConceptReference> resolveOneHit(ResolvedConceptReference hit) throws LBException{
	List<ResolvedConceptReference> returnList = new ArrayList<ResolvedConceptReference>();

	CodingSchemeVersionOrTag tagOrVersion = new CodingSchemeVersionOrTag();
	if (hit.getCodingSchemeVersion() != null) tagOrVersion.setVersion(hit.getCodingSchemeVersion());

          CodedNodeGraph cng = null;

          if (lbSvc == null) {
		return null;
	}


		cng = lbSvc.getNodeGraph(
			hit.getCodingSchemeName(),
			tagOrVersion,
			null);

          Boolean restrictToAnonymous = Boolean.FALSE;
          cng = cng.restrictToAnonymous(restrictToAnonymous);

          LocalNameList localNameList = new LocalNameList();
          localNameList.addEntry("concept");

          cng = cng.restrictToEntityTypes(localNameList);


	if (_associationNameAndValueList != null) {
		cng =
			cng.restrictToAssociations(
				_associationNameAndValueList,
				_associationQualifierNameAndValueList);
	}

	else {
		String scheme = hit.getCodingSchemeName();
		SimpleDataUtils simpleDataUtils = new SimpleDataUtils(lbSvc);
		boolean isMapping = simpleDataUtils.isMapping(scheme, null);
		if (isMapping) {
			NameAndValueList navl = simpleDataUtils.getMappingAssociationNames(scheme, null);
			if (navl != null) {
				cng = cng.restrictToAssociations(navl, null);
			}
		}
	}

	ConceptReference focus = new ConceptReference();
	focus.setCode(hit.getCode());

	focus.setCodingSchemeName(hit.getCodingSchemeName());
	focus.setCodeNamespace(hit.getCodeNamespace());

	LocalNameList propertyNames = new LocalNameList();
	CodedNodeSet.PropertyType[] propertyTypes = null;
	SortOptionList sortCriteria = null;

	ResolvedConceptReferenceList list =
		cng.resolveAsList(focus,
			_resolveForward, _resolveBackward, 0,
			_resolveAssociationDepth, propertyNames, propertyTypes, sortCriteria,
			_maxToReturn);

	for(ResolvedConceptReference ref : list.getResolvedConceptReference()){
		if (ref.getSourceOf() != null && this.getAssociations(ref.getSourceOf()).size() > 0) {
			returnList.addAll(this.getAssociations(ref.getSourceOf()));
		}

		//if(ref.getSourceOf() != null){
		//	returnList.addAll(this.getAssociations(ref.getSourceOf()));
		//}

		if (ref.getTargetOf() != null && this.getAssociations(ref.getTargetOf()).size() > 0) {
			returnList.addAll(this.getAssociations(ref.getTargetOf()));
		}
		//if(ref.getTargetOf() != null){
			//returnList.addAll(this.getAssociations(ref.getTargetOf()));
		//}
	}
	return returnList;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
public static Vector resolveIterator(ResolvedConceptReferencesIterator iterator, int maxToReturn, String code)
{
	Vector v = new Vector();
	if (iterator == null)
	{
		_logger.debug("No match.");
		return v;
	}
	try {
		int iteration = 0;

		Util.StopWatch stopWatch = new Util.StopWatch();
		while (iterator.hasNext())
		{
			iteration++;
			iterator = iterator.scroll(maxToReturn);
			ResolvedConceptReferenceList rcrl = iterator.getNext();
			ResolvedConceptReference[] rcra = rcrl.getResolvedConceptReference();
			for (int i=0; i<rcra.length; i++)
			{
				ResolvedConceptReference rcr = rcra[i];

                   //org.LexGrid.concepts.Concept ce = rcr.getReferencedEntry();
                   org.LexGrid.concepts.Concept ce = new org.LexGrid.concepts.Concept();
                   ce.setId(rcr.getConceptCode());
                   ce.setEntityDescription(rcr.getEntityDescription());
                   
				if (code == null)
				{
					v.add(ce);
				}
				else
				{
					if (ce.getId().compareTo(code) != 0) v.add(ce);
				}
			}
		}
		long duration = stopWatch.duration();
		_debugBuffer.append("DBG: " + stopWatch.getResult(duration) + " * resolveIterator\n");
           _excelBuffer.append(stopWatch.getSecondsString(duration) + "\t");
	} catch (Exception e) {
		e.printStackTrace();
	}
	return v;
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
@Test
   public void testViewInHierarchy() throws Exception {
    int m = 0;
    csVec = codingSchemeDataUtils.getCodingSchemes(true); // excludeMappings
    RandomVariateGenerator rvGenerator = new RandomVariateGenerator();

    System.out.println("Number of coding schemes: " + csVec.size());
       int lcv = 0;
       for (int i = 0; i < csVec.size(); i++) {
           String t = (String) csVec.get(i);
           System.out.println(t);
           Vector u = StringUtils.parseData(t);
           String scheme = (String) u.elementAt(0);

           if (scheme != null && scheme.compareTo(gov.nih.nci.evs.browser.common.Constants.NCI_METATHESAURUS) != 0 &&
               !Arrays.asList(gov.nih.nci.evs.browser.common.Constants.TERMINOLOGY_VALUE_SET_NAMES).contains(scheme)) {
			String version = (String) u.elementAt(1);
			if (metadataUtils.tree_access_allowed(scheme, version)) {
				lcv++;
				System.out.println("(" + lcv + ") " + scheme + " (" + version + ")");
				long ms = System.currentTimeMillis();
				ResolvedConceptReferenceList rcrl = testCaseGenerator.generateTestCases(scheme, version, ServiceTestCase.SAMPLE_SIZE,
													TestCaseGenerator.TYPE_TERMINOLOGY);
				if (rcrl == null || rcrl.getResolvedConceptReferenceCount() == 0) {
					m++;
					System.out.println("\tERROR: generateTestCases failed.");
				} else {
					int sel_case = rvGenerator.uniform(0, rcrl.getResolvedConceptReferenceCount()-1);
					ResolvedConceptReference rcr = rcrl.getResolvedConceptReference(sel_case);
					String name = rcr.getEntityDescription().getContent();
					String code = rcr.getCode();
					String namespace = rcr.getCodeNamespace();

					System.out.println("code: " + code);
					System.out.println("namespace: " + namespace);

					try {
						String jsonstring = getJsonString(scheme, version, code, namespace);
						System.out.println("\t" + jsonstring);
					} catch (Exception ex) {
						ex.printStackTrace();
						System.out.println("\tERROR: Unable to create View in Hierarchy JSON string.");
						m++;
					}
				}
				System.out.println("Total run time (ms): " + (System.currentTimeMillis() - ms));
			}
			System.out.println("\n");
	    } else {
			System.out.println("(*) " + scheme + " -- Tree not available.");
		}
	}
	assertTrue(m == 0);
}
 

import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList; //导入方法依赖的package包/类
/**
 * Attempt to approximate compositional or sub-query match (e.g., "peptic ulcer"
 * will match the two separate concepts for "peptic" and "ulcer", in case the
 * ontology does not contain any concept matching the full text "peptic ulcer").
 * @param s The test string.
 * @param lbSvc
 * @param scheme
 * @param csvt
 * @throws LBException
 */
protected void matchSubquery(String s, EVSApplicationService lbSvc, String scheme, CodingSchemeVersionOrTag csvt)
	throws LBException
{
	Util.displayMessage("\n*** Subquery match (incorporates partial normalization/stemming).");

	// Similar to synonym match, only allow match on any single non-stop word
	// and only print presentations matching the query.
	//
	// On resolve, we sort by lucene score ('matchToQuery' sort algorithm).

	StringBuffer searchPhrase = new StringBuffer();
	String[] words = toWords(s, true);
	for (int i = 0; i < words.length; i++) {
		if (i > 0)
			searchPhrase.append(" OR ");
		searchPhrase.append(words[i]);
	}

	// Define the code set and add restrictions ...
	CodedNodeSet nodes = lbSvc.getCodingSchemeConcepts(scheme, csvt);
	nodes.restrictToMatchingDesignations(
		searchPhrase.toString(), SearchDesignationOption.ALL, "StemmedLuceneQuery", null);
	SortOptionList sortCriteria =
		Constructors.createSortOptionList(new String[]{"matchToQuery"});
	PropertyType[] fetchTypes =
		new PropertyType[] {PropertyType.PRESENTATION};

	// Resolve and analyze the result ...
	ResolvedConceptReferenceList matches =
		nodes.resolveToList(sortCriteria, null, fetchTypes, -1);

	// Found a match?  If so, print each associated presentation containing at least
	// one word from the query expression (exclude non-matching synonyms).
	if (matches.getResolvedConceptReferenceCount() > 0) {
		for (int i = 0; i < matches.getResolvedConceptReferenceCount(); i++) {
			ResolvedConceptReference ref = matches.getResolvedConceptReference(i);
			printText(ref, words, 1);
		}
	} else {
		Util.displayMessage("\tNo match found.");
	}
}